184 Whole-transcriptome analysis by RNA-Seq for genetic diagnosis of Mendelian skin disorders in the context of consanguinity

Abstract

Among the ∼8,000 Mendelian disorders, over 1,000 of them have cutaneous manifestations. In many of these conditions, the underlying mutated genes have been identified by DNA-based techniques, which, however, can overlook certain types of mutations, such as exonic-synonymous and deep-intronic sequence variants. Whole-transcriptome sequencing by RNA-Seq can identify such mutations and provide information of their consequences. We have analyzed the whole transcriptome of 40 families with different types of Mendelian skin disorders with extensive genetic heterogeneity. The RNA-Seq data were examined for variant detection and prioritization, pathogenicity confirmation, RNA expression profiling as well as genome-wide homozygosity mapping in the case of consanguineous families. Among the families examined, RNA-Seq was able to provide information complementary to DNA-based analyses for exonic and intronic sequence variants with aberrant splicing. In addition, we tested the possibility of using RNA-Seq as the first-tier strategy for unbiased genome-wide mutation screening without information from DNA analysis. We found pathogenic mutations in 35 families (∼88%) with RNA-Seq in combination with other NGS methods, and we successfully prioritized variants and found the culprit genes. In addition, as a novel concept, we propose a pipeline that increases the yield of variant calling from RNA-Seq by concurrent use of genome and transcriptome references in parallel. Our results suggest that “clinical RNA-Seq” could serve as a primary approach for mutation detection in inherited diseases, particularly in consanguineous families, provided that tissues and cells expressing the relevant genes are available for analysis.